Pull Request Checklists

This document contains checklists for dealing with PRs. More general PR information is available at Pull Requests.

Reviewing Pull Requests

This checklist is to be kept in sync with the checklist in the pull request template.

When reviewing a PR, do the following:

  • Make sure it is coming from issues/XXXX-fix-the-thing in the Toil repo, or from an external repo.

    • If it is coming from an external repo, make sure to pull it in for CI with:

      contrib/admin/test-pr otheruser theirbranchname issues/XXXX-fix-the-thing

    • If there is no associated issue, create one.

  • Read through the code changes. Make sure that it doesn’t have:

    • Addition of trailing whitespace.

    • New variable or member names in camelCase that want to be in snake_case.

    • New functions without type hints.

    • New functions or classes without informative docstrings.

    • Changes to semantics not reflected in the relevant docstrings.

    • New or changed command line options for Toil workflows that are not reflected in docs/running/cliOptions.rst

    • New features without tests.

  • Comment on the lines of code where problems exist with a review comment. You can shift-click the line numbers in the diff to select multiple lines.

  • Finish the review with an overall description of your opinion.

Merging Pull Requests

This checklist is to be kept in sync with the checklist in the pull request template.

When merging a PR, do the following:

  • Make sure the PR passes tests.

  • Make sure the PR has been reviewed since its last modification. If not, review it.

  • Merge with the Github “Squash and merge” feature.
    • If there are multiple authors’ commits, add Co-authored-by to give credit to all contributing authors.

  • Copy its recommended changelog entry to the Draft Changelog.

  • Append the issue number in parentheses to the changelog entry.